


Project Remus

by Mmjohns



Series: Non-cannon Relationship shorts [15]
Category: Agents of S.H.I.E.L.D. (TV), Marvel Cinematic Universe, The Avengers (Marvel) - All Media Types
Genre: AU, F/F, F/M, Multi, Project Remus, Wolf Pack
Language: English
Status: In-Progress
Published: 2016-03-27
Updated: 2016-07-01
Packaged: 2018-05-29 10:05:02
Rating: Mature
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 25
Words: 10,580
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/6370552
Author URL: https://archiveofourown.org/users/Mmjohns/pseuds/Mmjohns
Summary: <blockquote class="userstuff">
              <p>Skye finds herself captured by shield and trained at the SHIELD SCI-TECH academy to take part in something called operation Remus a series of interconnected segments designed to give narrative to this tale completely AU</p>
            </blockquote>





	1. Premise

Flashback story made of small interconnected memories which may one day be expanded based on the tale of Skye as she gets involved with something called Project Remus


	2. May 12th 2007

It wasn't the first time some guy in a suit had come to pick Skye up for allegedly hacking something.

Although, this was the first time they could prove anything.  
This bag over her head certainly put a different slant on the world  
The bag comes off her head roughly, and she finds a man standing before her  
"Hello, my name's Phil Coulson, and I have an offer for you."  
The next few hours are spent with Coulson learning about this offer of his, apparently he wants her to join SHIELD, should be interesting, but most interesting is this project he wants her for, Project Remus


	3. May14th 2007

The door to her new room swung open "Huh, nice place; Coulson wasn't kidding when he said they had the best toys."

Then from behind comes a voice "Hello there, I'm Jemma Simmons."

"Skye, just Skye."

"Well nice to meet you, Skye, it appears I'm your new roommate."

"Awesome, Coulson told me about you, said you would be able to keep up, it's going to be pleasant to have someone to talk to that understands what I'm saying."

"Why? Don't people usually comprehend what you mean?"

"No, something about having an IQ in the order of 190, most people can't keep up or think I'm just condescending or sarcastic, although I was told that wouldn't be an issue with you."

"I shouldn't think so, besides we'll find out soon enough there's a reason we're bunking together, and I get the feeling it's the same reason we both have to take operations classes."


	4. September 22nd 2007

Coulson had said his friend/ex-partner was crazy but Melinda May undoubtedly went above and beyond that, for an admin clerk she was crazy good at this stuff, no wonder Coulson had insisted she be her SO, then again God knows why he had requested she took operations training when she was enrolled at communications.

"Again, and stop daydreaming."

The woman was cold as ice, but eventually, now and then a little sliver of happiness would peak out when Skye got something right or managed to do something particularly funny.   
That was what kept her going, what kept her coming back every week like some glutton for punishment training and getting thrown on her back because every now and again she could see the person Melinda May pretended not to be. That and somehow Coulson had talked her into becoming her SO, and she'll be damned if she lets Coulson down after he's gone to bat for her.

Moving quickly she strikes out managing to catch May off guard slightly and land a glancing blow on her arm

"Good, you might just make it into Remus after all, again."


	5. July 20 2008

"But May, you never come out with us, besides Jemma said she's bringing her SO along as well so you'll have someone to talk to."

"Simmons is bringing her SO as well, you're sure?"

"Yep, apparently it was her idea to go out for this, God knows it wasn't Jemma's."

"In that case, I will come, even if it's only to stop you and Natasha raising Hell together."

"Natasha?"

"My old rookie and Simmon's SO, you two are so similar sometimes it gives me a headache, and I have nightmares thinking about what would happen if you two decided to raise hell together."

"She sounds cool, can't wait to meet her."

"Ok, but there's one condition you wear an interdiction bracelet, I can't have you drunk hacking again."

"Fine" Skye sighs

 

///-////////  
"No, I don't want any part of your bad girl shenanigans."

"But Jemma" Skye and Natasha groan together

As May had predicted Skye and Natasha had hit it off like a house on fire., It had taken less than 2 minutes after May had left for them to start trying to get Simmons to help them hack Tony Stark's mainframe.   
Eventually, however, it was time to go and just as they are about to leave Skye leans over and gives Natasha a quick peck on the cheek saying "Thanks, Red this was fun we should do it again sometime" before turning to leave, leaving a stunned biochemist and a confused redhead in her wake

 


	6. December 17th 2008

For most graduation from the academy was a source of celebration and an excuse to go out with one`s fellow agents and get hammered, not for Skye. Simmons had graduated a month and a half earlier due to her previous schooling, joining Project Remus straight out of the academy and making friends with Leo Fitz. 

Now it was Skye's turn to finally find out what she had been training for all this time, to discover the path she had picked out for herself.

May looked down at the young woman before her "Skye are you sure this is what you want, no one would hold it against you if you wanted to back out."

"No, I want, no I need to do this."

"Very well, you must choose a sire from those you see before you, one to share their blood with you and bring you into the pack, they have all offered themselves for this, but the choice remains yours."

The group was small maybe only a dozen all up but only one person caught her eye "Natasha, I choose Natasha."

The lithe redhead stepped forward and without warning started to change until before them stood a beautiful red she-wolf with piercing green eyes. Skye kneels slowly and bares her neck to the wolf before her, as the wolf sinks its teeth into her flesh Skye begins to shake and falls to the floor a change rippling throughout her body as she lay beneath the moonlight. Eventually, her body stilled and instead of seeing Skye laying there, there lay a small white pup which instantly moved over to the red she-wolf and lay snuggled into her side


	7. December 18th 2008

When Skye awoke, she found herself curled around a certain redhead and snuggled tightly into her chest, letting out a small groan she has barely moved before Natasha swings one arm over her mumbling something that sounds suspiciously like "Stay…Skye …please…stay"  
As she rolls back into the redheads, embrace she can't help but feel a sense of contentment and happiness wash over her just before sleep overtakes her.

Sitting across from them Coulson and May watch the two interact a small frown on Coulson's face, May looks at him and says "let it go, Phil, there's nothing you could do, I knew the second that I saw her they'd end up together one day."

"Yeah but it still feels wrong Mel, she's like my Daughter."

"Phil, we were both there last night, you saw the way Skye was. She was drawn to Natasha just as I was to you. She didn't even see anyone else; there's no way anything else was ever going to happen, or that she'd end up with someone else, you know as well as I do, our wolves have a way of knowing what we need well before we do."

"That doesn't mean I have to like them all snuggled up like that."

"You didn't mind when it was us doing the snuggling, speaking of which what say we give them a little privacy before they have to get back into the pack life and do some snuggling ourselves."

"Ok, I can't believe everyone I know is scared of you, you big softie" Coulson teases walking back toward their rooms and leaving Skye and Natasha snuggled tightly in the living room


	8. December 25th 2008

Apparently Christmas was a big thing in the pack, more so when there had just been a new inductee. Skye had spent the last week dividing her time between laying in Natasha's arms and running through the Vale with her. In the week since her awakening as they called it, (because yes apparently she already had his ability inside her it just had to be awakened) her wolf had grown substantially. So much so that she was nearly Natasha's size when transformed, and the transformation was both at will and significantly easier than it had been. Something that by all accounts should not have been possible, something that typically only ever happened to the pup of an Alpha.  
The rest of the pack was pretty cool they all seemed rather chill for SHIELD agents, then again that could partly be due to the semi-telepathic connection she seemed to share with them, again something that by all rights belonged only with the Alphas.

She has barely sat down after coming back from a hunt with Nat before there is a knock at the door and May enters "Skye we need to discuss something."

"What is it?"

"Tonight we will be joined by another pack, led by Victoria Hand; she is likely to be quite gruff and rude toward you."

"Ok, I'll ignore her then."

That's, exactly, what you can't do. You may not realise this yet, but there is a distinct hierarchy amongst the packs ours is always known to have the strongest members. Add to that that you a week old are already as advanced as a much older wolf, and we appear even tougher. She will seek to weaken us by embarrassing you; you can't let her."

"So what you want me to beat her?"

"If it comes to that, yes. Tell me do you know the purpose of a Beta within a pack, why you and Natasha, two Betas, are drawn so powerfully to each other?"

"No, I hadn't honestly thought about it."

"In a pack the Alphas breed and control who may enter the pack, in our case, we decide who is to be awakened. Omegas like Jemma, Leo, Bobbi and Trip are the ones who raise the pups; in typical cases, a newly awakened pup is given over to them to train and teach our ways. Betas are the Warriors they represent the guardianship of the pack and protect the other members from harm and enforce the rules of our society. You and Natasha are Betas, you are naturally protective and highly skilled, in the event of the death of an Alpha, a Beta will take their place and an Omega theirs. However you and Nat are different, you are bonded mates meaning the only way you ascend to Alpha is together, but it also means you're significantly stronger than the other Betas out there, even separated your bond allows you a greater protection than any other Beta. Victoria will seek to undermine this, you, can, not, let, her, understood?"

"Yes May"

/////----//// later that night

"Ahh Melinda, Phil nice to see you, and this must be your new pup doesn't look like much, take my coat Pup," Victoria says holding out her coat 

Before Phil can reply Skye has already stepped forward "take your own damn coat unless you're too much of an invalid to do so, then I suggest you step down and let your Beta's take command."

There's a shocked silence as everyone watches with baited breath as the two wolves stare at each other until suddenly Victoria moves to slap Skye. Before anyone else can even react, Skye has moved, shifted into her wolf form, and leapt forward; pushing Victoria onto her back and lightly grabbing hold of her throat a paw on either side of her head.

Finally recovered Melinda says "Skye, let her go."

Skye steps back and immediately she is back in human form standing like the events of the past few minutes haven't happened, Victoria, on the other hand, remains on the ground where Skye had left her still shocked at her complete domination by the young Beta

Phil looks at Victoria before saying "now I assume you won't be making that mistake again Victoria you're very lucky you didn't lay a hand on Skye else your pack would be looking for a new Alpha."

"How dare you, I don't have to stand for this, we're leaving" she yells at Coulson before turning to her pack "come on."

Not a single member of her pack moves to follow. Instead, they look at Skye and Natasha, who have moved to stand beside Melinda. 

Maria Hill Victoria's Beta says "no, we don't follow you anymore Skye was right, you've grown weak, Skye you won in combat against her. We stand ready to support you."

All eyes turn to Skye all those except for Natasha, and that is only because she and Skye have been conversion Psychically this whole time "I appreciate the offer, but I follow Coulson and May if they agree I would like to integrate you into the pack, but I cannot leave my Pack."

Coulson and May exchange a few looks before they say "we would love to have you all as a part of our pack."

Maria and the rest of her pack fall to their knees and bear their necks as Coulson and May walk past them one by one placing a hand on their bite marks establishing the neurological bond that all pack mates eventually share

As soon as they are done Natasha looks at the now significantly larger pack and says "we're going to need more food, come on Skye let's order some" before pulling Skye away towards the mess hall


	9. March 17th 2009

When Clint walks onto the firing range on the Helicarrier one morning he hadn't expected to find anyone here but the last thing he had expected was to find was a small half Asian girl almost the spitting image of Melinda May hanging upside down from the rafters bow in hand shooting targets with one eye blinded.

"Are you going to stand there all day Agent Barton or are you going to do what you came here to do, May says you're the best with a bow let's see if she's right."

Smirking he walks over to the window and pulls his bow ready to show her just who she's up against  
Several hours later and with a massive crowd given the fact it's the middle of the day Barton can't help the groan as the young agent bests him again, something no one else has ever been able to do

"Come on, one more round."

"Sorry Barton but any longer and May will be looking for me; I have to go if I want to get home to my girlfriend tonight."

As she walks off, he can see the bright grin on her face and the groan of the numerous agents who had apparently lost money betting on the results of their little match


	10. March 17th 2009 Part 2

As she lay in bed, that night she turned to the redhead beside her and said: "you know he's going to figure it out eventually Nat."

"Barton might be decent, but he's nothing compared to May or us."

"Yeah, but Coulson knows, and we all know that after a few drinks Coulson can slip a bit."

"Yeah, but that's why we don't let Coulson drink without May there anymore."

A smile appears on Skye's face as she leans over whispering into Nat's ear "so which do you want handcuffs or chains?"

"Surprise me," Natasha says as she feels her girlfriend pull her hands up and toward the headboard


	11. March 27th 2009

"She's what!!"

"She's dating Skye."

"What? How did I not know this?"

"Because it was none of your business."

"But she's my partner how in Hell, did I miss this."

"Come on, Barton, we both know that when it comes to May and Natasha, you and I aren't even   
in the same league let alone at the same skill level."

"Yeah, but, how did I not catch anything."

"As I said they're good, and there's a reason Skye is May's trainee, she was good before the academy, she was great at the academy, she's only getting better, wouldn't surprise me if she ends up being the director one day."

"Fuck, I haven't even given the shovel talk yet."

"I wouldn't even try Clint, as I said there's a reason Skye and May do so well together. You know how they always say that eventually you train the agent that will replace you, well that's what Skye is to May. That and as you know Skye is part of the Pack, she's more than capable of tearing you a new one."

"Come on Phil; she's barely a pup."

"She's Natasha's mate and a Beta to boot; I wouldn't try it, Clint."

"A Beta? How did she get that high already?"

“There's a reason we brought her in in the first place Clint, besides being the best hacker we have ever heard of she has the strongest concentration of the Remus gene I've ever heard of besides May, what took us years to learn is natural to her."

"Well, crap."

"Ah huh."

"So don't piss her off?"

"Yep"


	12. March 28th 2009

"Skye, Natasha you're late."

"Sorry May, Nat and I got held up; Hawkeye was hiding in the vents outside our room this morning."

"Well you should have thought of that before you tried to hide this from him, both of you on the mat, today you're sparring, and if I find out either of you are holding back, I'll tell Barton myself."

They line up on the mat one on either side Natasha towering over Skye then May signals, and they immediately launch into a flurry of blows back and forth strike and counter-strike flowing like two well-practiced dancers engaged in a perfectly synchronised dance back and forth neither giving nor taking an inch. Eventually, they both fall to the mat exhausted as May stands watching, a smirk on her face at her two protégés.


	13. March 30th 2009

The Director could hardly believe his eyes as he watched the video from the training room as Romanoff and Skye sparred under the watchful eye of Agent May, it was a beautiful thing to behold as they went back and forth

From over his shoulder he hears Hill's voice "she's ready, she's as good as Romanoff or May."

"Yes, but you tell that to Romanoff, I can't see her being happy with this."

"She doesn't need to be happy, we need Skye for the Rising Tide mission, she knows the job, hell we all have to do things we don't like."

"Yes, but it makes life easier if she is happy, an angry Black Widow can be a right pain in the ass."

"Indeed, we could send her and Barton on a mission."

"No, we'll give them two weeks and then send her under, have Coulson run back-end and begin setup for operation T.A.H.I.T.I."

"What do we tell the Pack."

"Nothing, they can't know, it's the only way to keep them all safe."

"They aren't going to like losing a Beta, let alone without a good reason, hell I don't like the thought of it, and I know why."

"I know, but there's no other choice, it has to be Skye she's the only one who can do it."


	14. April 20th 2009

"I hate this Mel, I hate not knowing if she's ok or not; I hate not being able to do something."

"I hate it too Nat, but this is the job, how do you think I feel whenever Phil goes somewhere for Fury without me being able to help."

"Yes but you at least know where he is and what's going on, Fury won't give me anything but she's infiltrated a hacker collective, and when I ask Coulson he just tells me to trust the system."

"Nat, you can't know, you're not technically anything to each other, you didn't want everyone to know, this is the price you pay, besides it's not just you, it's the entire Pack, either way, Fury isn't talking."

Natasha pauses a moment at this "What if I did want people to know" she asks before placing a small blue box on the bar

Looking at the case in front of her Melinda asks "Natasha is that what I think it is."

"Yes, I love her Mel. God help me, I know love's for children and I know it's only been a year, but I love her. I don't know what I'll do if I lose her, it tears me apart not to know what's happening to her, I can feel a part of myself slowly dying."

"I'll see what I can do, but there are no promises, Natasha, besides you need to get some sleep before you have to fetch Banner in the morning."


	15. May 17th 2009 (5 days after the battle of New York)

"Goddammit Nick, do you have any idea what the hell you've done? Coulson should never have been on that helicarrier and you know it kills me to say this, but you should never have used T.A.H.I.T.I on him it was everything he was against." Melinda yells before heavily sighing, continuing. "and you won't even let us bring Skye back in She was like a daughter to us. Hell, I'm pretty sure she's the only one Natasha has ever truly loved, and you won't even let us bring her back in from the cold. What could this group possibly be doing that's so much more important than her being here with her family."

"Melinda they were trying to hack Project Remus."

"What!!! They attempted to hack Project Remus, and you didn't tell me! You know what type of danger this puts the pack in, hell you sent Skye in there alone knowing they were looking for us."

"Melinda there's no way to know Skye's a wolf, she was never logged into the system; there are no records of her ever even being brought into SHIELD everything about her from her name to her clearance level was deleted as far as SHIELD is concerned Agent Skye never existed."

"Really, Nick? that's just supposed to make everything better, all that means is that if they find her out she has no backup, you wait until I tell Natasha about this you'll lose the other eye."

"She has a safeguard, a code phrase that will give her immediate assistance whenever she needs it and a chip containing a copy of her file, scrubbed of all mention of project Remus but guaranteed to get her access to whatever becomes necessary."

"I don't care, Nick, I want her back, soon, or so help me, I'll get her myself."

"Fine, fine, I'll bring her in, on one condition."

"Name it."

"I'm assembling a team to look after Coulson; I want you to lead it. As far as he will know I am putting him in charge, but you will report directly to me if he starts showing side effects from the treatment, in exchange I'll bring Skye in. She will be assigned to the same unit as a consultant, one of the people I'm assigning you, Grant Ward is worrying me, and I want you and her to keep an eye on him."

"Let me get this straight; I spy on the man I love while simultaneously acting like the girl I think of as a daughter means nothing to me. While she works like some nobody, instead of the skilled agent she is, instead of acting like the level 8 agent she is and thereby putting herself in danger. All so she can watch some Specialist, and in exchange, you bring her out of somewhere you should never have sent her into in the first place."

"Pretty much."

"Ok I'll do it, but so help me, Nick, if this goes Pear shaped you and I are going to have a chat, and you won't like the results."

"Agreed"

"And assign the Pack to our home base, they miss Skye, the absence of our Beta has been hard on the others especially Natasha, I wouldn't want to be in your shoes if you don't."

"I'll make the arrangements."


	16. May 22nd 2009 (10 days after battle of New York)

The message from May was quite short "Coulson inbound for extract, do not reveal Identity, await further instructions."

The bag was a déjà vu moment, though, hell it seems whenever she's brought back to shield it's with a black bag over her head. If they didn't want her to know where they were or where they were going they should have done a better job, hell her intensified wolf senses mean she could find her was across the country in the middle of a blizzard during a moonless night, a bag was nothing. Although the most unnerving thing is for the last ten days, she hasn't been able to feel Coulson.

She had assumed it was to do with distance and time spent apart, but it wasn't getting better. She could smell him and hear him as he sat in front of her but it wasn't him, well it was, and it wasn't he still seemed the same but the things that made him a wolf; the smell, the feeling that she got off other wolves was gone. It was like he had been replaced by an empty shell like someone had taken everything he was and removed it then tried to stuff only some of it back inside, it was terrifying.

When they arrived at the plane her worst fears were confirmed she could feel the others around her she could feel May, Fitz and Simmons but not Coulson, she could feel the pack nearby but no matter how she tried she couldn't sense Coulson 

When they entered the interrogation room, it truly was a sense of déjà vu as the first interrogation replayed nearly word for word. But for this Ward asshat, geez how she'd like to bust his self-important bubble. If he only knew who he was sitting across from he'd be a stuttering mess by now., But, she had her orders, and she'd be damned if she wasn't going to follow them to the letter


	17. May 27th 2009 (15 days since battle NY)

The mission had been relatively straightforward up until she had been kidnapped, but overall, the worst part was having to act like those that she cared for meant nothing to her. The mission may have been easy, and she may be a capable liar but for Skye the fact that she couldn't even spend time with the family she had grown into hurt more than any wound.

Luckily for her Coulson had offered her a position as a consultant, this was good in that it brought her closer to her family, Natasha was nearby but for some reason she was keeping her distance, maybe the same reason Coulson didn't know who she was anymore, either way, it hurt.

Luckily when she went down to the labs that evening after dinner there was no one else there besides Fitzsimmons, May having agreed to be her shadow was, naturally, with her, so she knew Ward and Coulson wouldn't be watching.   
.Without hesitation she immediately launched herself at them, pulling Simmons and Fitz into a deep hug and starting to berate them for not coming to see her. That was until she remembers who's behind them right now and launches herself into May's now waiting arms mumbling her apologies about Coulson, and assurances, they'd find a way to get their Coulson back. As she held May she felt her Alphas tears for her lost mate and knew what had happened; Coulson may have rejoined the land of the living, but he wasn't truly back. 

After a few minutes, May says "Natasha asked me to tell you, she's waiting for us at the new base, as soon as we're finished with this 084 we're heading there, and apparently she isn't letting you go anywhere ever again."


	18. June 1st 2009

The Peruvian 084 had been interesting, to say the least, hell it had nearly caused the deaths of 4 of the people she cared for deeply so naturally Skye had hacked into SHIELD and arranged for this cruel thing to be sent to the slingshot just like everything else The Pirate had been hoarding.

Let's face it calling him The Pirate was damn accurate; he had one eye and a tendency to stockpile dangerous and powerful objects; all he needed now was a parrot and a peg leg, and there'd never be any room for further argument "maybe she'd send him one for Christmas this year. Anyway, that could wait she could practically feel the tension coming of Tasha as she got closer and knew the moment they touched down she'd be heading straight for her and their rooms, not to leave for several days

A collective groan escaped Fitzsimmons and a small smirk rested on May`s mouth as she looked at Skye with a raised eyebrow, "crap, really gotta learn to stop broadcasting my feelings and thoughts again."

May's smirk only increases as she hears Natasha's voice saying "yes darling you do, not that I don't agree with the sentiment, but unless you want to scar Fitzsimmons for life, you need to start shielding yourself again."


	19. June 3rd 2009

When Skye and Natasha finally emerge from their room, there`s a collective sigh of relief from the entire pack. Needless to say, no one had been getting much sleep over the last couple of days, but they were sympathetic to their friend's pain at being separated. Hell a couple of them even knew what Natasha had planned for after the meeting they were having that afternoon. That being said it would be good to get some proper uninterrupted sleep for the first time in two days.

\---///---///  
That afternoon the pack meets in one of the old hangars buried up the back of the base while allegedly being used for storage they had arranged it, so they had a nice large area for them all to hang out in as a pack and hold their meetings.

"Ok everyone quiet." May calls "First order of business, welcome back Skye I'm sure everyone is happy to finally have you back."  
There's a loud round of cheering and applause, and once it stops Melinda continues. "now, unfortunately, there is something more to discuss, as you are all undoubtedly aware Phil is no longer a wolf. He was killed and to bring him back his wolf sacrificed itself; there is a way to bring him back but he can never be an Alpha again, and by law as his mate neither can I."

"Then what happens?" Bobbi Morse calls from her lounging position at the rear of the group

"There are two options either Skye and Natasha as the head Betas ascend to become Alphas, or, and this pains me greatly, we leave Phil as a man and don't include him in the wolf business. Skye, Nat how do you feel about this?"

"You say it's the only way." Natasha asks looking at Melinda 

"Yes, it's the only way Phil can ever become a wolf again."

Skye and Natasha share a look a moment before Skye says "Phil did so much for me. I wouldn't be here today if he hadn't helped me. If this is what it takes to bring him back into the fold then so be it, but, you have to agree to help us. Neither Tasha or I have ever done anything like this before."

"Agreed, then we are decided as of this moment Natasha and Skye are the Alphas of the Pack."

Everyone else nods and as they rise to leave Natasha looks at them all saying "before you all leave there is something else."  
then turning to Skye she says "Skye, my beautiful Skye, there is something I have wanted to ask for a while now, and I know we haven't been together long, but I can't imagine ever not feeling this way,"  
Then getting down on one knee "what I am trying to say, Skye, is that I love you. You complete me, and I can't imagine trying to live my life without you in it, will you marry me?"

Skye looks down at the redhead before her and sees the absolute love in her eyes, at that moment, she couldn't care less about the world around them all that matters is their love. Smiling and with tears in her eyes she drops to her knees and pulls Natasha into a hug saying "yes, I'll marry you, I love you, I'd love to spend the rest of my life with you."


	20. June 7th 2009

The last few days had been hectic, to say the least, between the missions for Coulson, the Avengers and the new requirements of being Alphas of the Pack; everything else had been temporarily swept aside, but finally, the day had come. While neither one particularly wanted a fancy wedding because they were Alphas now and it was expected Skye, and Natasha stood at the foot of the Vale were the Remus Base was hidden, as the pack surrounded them. Their Beta Maria Hill stood as the officiant and before them the entirety of the pack awaited the union they were there to witness. As they stood before the pack, Skye couldn't help but stare at the redheaded beauty before her, entranced by the visage that was her mate. 

While, not ones for pomp and over the top celebration the pack was one for tradition, something that over the last century had kept them safe and maintained continuity from one generation to the next

As they exchange vows the tears flow freely from their pack-mates who stand watching fixated on the ceremony and finally in the conclusion of the ceremony both change into their wolf forms and move towards the nearby tree line that marks their trek together towards the crest of the nearby mountains


	21. June 12th 2009

They had spent several days in the Vale until finally they were forced to leave In that time the others of project Remus had become aware of the changes within their pack and Melinda with the help of the others had re-birthed Phil's wolf. Unfortunately, however, for now, they had to go about business as normal separated for the majority of their days. The encounter with the berserker staff has caused significant strain, not only because of Melinda's exposure but because they had finally realised the reason Fury had assigned Ward to them and as much as she wished it wasn't the case Skye found herself being forced to confront the traitor about his loyalties.

The conversation had not gone well there had been yelling and screaming and fighting, and then Ward had managed to flee to the cargo hold grabbing a parachute and jumping off the plane before anything could be done.

And this had lead to the new conversation they were having with Fury well the conversation Skye was having with Fury unfortunately now the only people on board were wolves Skye had to assume command something that apparently surprised Fury greatly and when he is surprised Fury can become a right pain in the ass

"What do you mean escaped."

"He jumped out of the plane Director."

"He jumped? He just up and jumped out of a plane in transit?"

"Yes, he obviously decided it was the better option."

"Put Coulson on"

"No way Director, I'm in charge of this unit, therefore, it's my responsibility, I've released my file into the SHIELD servers as far as anyone is concerned I'm in command as a level 9 agent, all that would serve to do is to raise flags."

"Ok, fine but I'm grounding you all indefinitely. Something big is going on here, and I don't know what. I think SHIELD has been infiltrated, take your pack and make your way to Avengers Tower. I'm authorising you to read them in on the whole project. Then scrub every mention of it from SHIELD servers, we can't afford for this to get out."

"Yes sir, I'll have May set a course immediately."

"Good, and Skye"

"Yes Director"

"Congratulations on both counts, I'm happy for you "


	22. June 15th 2009 The fall of  SHIELD and Hydra

**Notes for the Chapter:**

> Hey, people just thought id let you know I've updated grammar and phrasing on this story, don't worry the story is still the same its just a bit better flowing IMHO. I used a tool called Grammarly I advise any budding writers to give it a go, its pretty good. but anyway here`s the next chapter, it is pretty short but I hope you enjoy

When they finally make it to New York and touch down at the airport, Skye can't help but feel slightly overwhelmed by the sights and smells of such a large city., The differences so vast from her last few weeks spent in more quiet areas such as the Vale and bases. She is quickly brought back to earth by the feeling of Natasha standing beside her and the warm comforting feeling her presence provides.

However it is short lived as Natasha says "Maria just called, she is having issues getting the pack separated from SHIELD, apparently having so many high-level agents become unavailable can be hard to explain."

"tell her to go into a file labelled A2404-658-26-Alpha. There`s a program there, tell her to enter authorization code Alpha-3-Delta-9-9-Kelo, that will take care of anything regarding the Pack and our records as well as scrub all pack members from the servers. Then tell her to get her butt here now I don’t care who asks what, just, get everyone from Remus away from Shield now. Fury sent me a message about an infestation problem within Shield and, Project Insight; we need everyone under the towers protection as soon as possible."

As Natasha moves off to make a call, Skye can't help but imagine the utter devastation the Insight Carriers could cause if released. She decides she has to take preventative action, pulling out her phone she activates a program she designed when she first came across the files for Project Insight. It causes a virus to launch through the SHIELD systems and into the helicarriers activating their self-destruct features, knowing that it will potentially kill hundreds but knowing it may save millions

As she sees the final countdown, she sinks to her knees and is in moments surrounded as the others try to figure out what`s wrong. 

Natasha kneels down beside her and asks “Skye, Darling, what is it.”

“I've done something horrible Nat.”

“shh..shh.. its ok Skye, baby tell me what you did.”

“I've killed them, Nat, I sent a self-destruct code to the Insight Carriers. I might as well have pulled the trigger myself.”

“shh….baby, it's alright…you did what you had to do; there`s nothing to be ashamed of.”

Looking at the ground, I say “But I killed them all Nat I didn’t even hesitate I just flipped a switch and killed them all…what if there were innocents there….Oh my god what have I done, I'm a monster.”

“Skye honey you're not a monster. You only did what was necessary; you had your orders protocol was limit any civilian casualties that’s what you did.” then lifting my chin, so I'm looking at her “Do you think I'm a monster? I've killed far more people than you, and I didn’t hesitate to do it.”

Finally meeting her eyes, I say “No, never, you didn’t have a choice, you were just following orders, but I I made the decision, I didn’t get any orders.”

“Then by your own logic, you aren't at fault. You were only following orders; you know as well as I do that for a senior agent protocols are standing orders. And like it or not that is what you are you did not have a choice.”

 

“I hate you.” 

Smirking infuriatingly she says “I know.”

I can't help smile a little at the smirk on her face as I was“No quoting Star Wars.”

What I hadn't expected was for her to reply in her most seductive tone “Yes master.”

It practically causes me to melt as I say “Damn it, Nat, you know what that voice does to me, get in the car before we end up spending the night here.”

In that same damned voice, she says “Yes mistress; your wish is my command” before getting up and walking to the SUV. And I'll be damned if there wasn’t a little extra sway in her hips as she does. Damn those bunks are looking real good right now


	23. June 15Th

Their arrival at Avengers Tower went surprisingly well, given the circumstances. They managed to get inside before they found themselves surrounded by Avengers but quickly that fell apart as they recognised Natasha and Barton realised who was there. 

Stark, on the other hand, being the pompous jackass he was, decided to make a big deal about it but was surprised when he found himself immobilised within his own suit.   
Skye holds up her phone Saying "Cool it Stark, we`re not here to cause issues. And we`re not here with Director Eyepatch. We need your help."

Steve steps forward Sharon Carter at his side as he says "What the hell is going on, we got a call saying there was an explosion at the Tri-skellion?"

"that was me, "Skye says looking sheepish

"What!! DO YOU HAVE ANY IDEA WHAT YOU HAVE DONE" yells, Steve

As Skye has tears appear in her eyes Maria steps in front of them saying "cool it, Captain. You have no idea what you're talking about."

Steve`s eyes bug out of his skull as Sharon looks between them and says "Oh crap Steve you’ve stepped in it now."   
Then turning to Maria says "I apologise for Captain Foot-In-Mouth. I'm Sharon, and I'm pretty sure we`re soulmates."

Maria looks at them shocked a moment before her fury turns back to Steve saying "and what do you have to say for yourself."

Steve at least has the common sense to hang his head slightly as he says "I'm sorry, I overreacted."

Glaring at him she says "Don't tell that to me, tell that to the woman you just put in tears." 

"Yes, Ma`am" then turning to Skye he steps forward and says  
"Ma`am I apologise, I completely overreacted. I have no right to pass judgement when I don’t know the reasons you made that call."

Looking to Natasha Skye nods slightly wiping her eyes and the redhead turns back to face Steve saying "Your apology is accepted, Captain. Although if you ever make Skye cry again, there won't be a place on earth for you to hide, understood?"

Looking at the anger in her eyes Steve nods quickly saying "Understood."

"Good then let's get everyone upstairs before the reporters catch wind of this."  
before nodding to Skye saying "might as well release Stark, don’t wanna leave him here for the media to gawk at."

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As they make their way upstairs, Sharon moves over to Skye and says "I'm sorry for Steve, he doesn’t always understand the calls we have to make as agents, especially the one's higher-ups have to make. He and I will be discussing this at length later."

"Thank you" then wrapping herself back into Natasha's embrace Skye says "I understand why he was angry. I hate myself for what I had to do, and I honestly can't see that ever changing."

"A little advice then, something my grandma Peggy told me; don’t think about the lives you had to take, think about the families you have saved, think about all those who you protected by making the choice. The pain will never go away, but it can get easier to live with."

Reaching over she pulls Sharon into a hug as she says "Thank you. Look out for Maria, she's been at this a long time and hides it well but she's in pain, I won't tell you why that’s up to her but just be there for her."

"I will, she's stuck with us now, whether she likes it or not."

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When they arrive in the common room, and as soon as they do Skye finds herself pulled into a hug as Darcy practically tackles her before moving over and punching Steve "so not cool, Captain Spangles."

Natasha and Maria froze at this unable to process entirely how to respond but are saved from the need to as Skye says "it's good to see you again too Darcy, how`s Jane?"

"She`s good, we moved into the tower. Apparently she and Thor are mated so that’s nice. I don’t have to worry about her quite so much" then looking at Natasha's she says " speaking of I understand you found someone as well, you always did have a thing for redheads."

Laughing slightly Skye pulls Natasha over by the hand and says "Natasha, Meet Darcy, we shared a few foster homes growing up. Darcy meet Natasha my soulmate."

"Pleasure to meet ya Red, you’ve got your hands full with this one "then winking slyly "in more ways than one I imagine."

Natasha smiles as Skye blushes and says "you`re right about that, hey what say you, and I get together and exchange stories about Skye at some stage."

"Oh god, please, no" groans Skye" I am never leaving you two alone together."

"Fine, fine, ruin my fun" then turning to survey the others Darcy says" so why haven't you Introduced me yet."

"Sorry Darce" then turning to her friends behind her she says "everyone this is Darcy, she's like my sister."

then turning back to Darcy, she says "on the left there is Phil Coulson and Melinda May, they’ve become like parents to me."

"It's nice to meet ya, glad to see Skye has had someone looking out for her."

Smiling Phil happily says "it's nice to meet you too."

Skye continues "next to them, is Jemma Simmons. She is our resident biochemist and my best friend since the academy." 

"Ahh, so you're the Jemma I've heard about then. Skye`s told me only good things."

Jemma smiles as she says "Skye`s told me a little about you too, it’s a pleasure to meet you."

Smiling back at Jemma Skye says "then next to Jemma on her right is Leo Fitz, engineer extraordinaire and all around awesome dude."

"Ahh, so you're the one who created those awesome dwarves."

Fitz`s jaw drops for a moment as he says "I am, and it’s a pleasure to meet you."

Skye squeals happily before quickly pulling Darcy a hug saying "Oh my god, I can't believe it, I'm so happy for you two."

At this everyone, else apparently catches on and starts congratulating them before Natasha says "Guys, give them some space. Why don’t we let them get to know one another first before we start crowding them."

There are groans of Fine and Ok, but it's Melinda's groan of "Fine but hurry up I want grand babies" that has everyone laughing and Fitz blushing an iridescent Scarlet

Darcy quickly pulls him towards the elevator saying "Jarvis, my floor please" before rolling her eyes at Skye as her sister gives her a double thumbs up

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The rest of the day goes relatively quickly as everyone meets and mingles with everyone else, the only one not there at the moment being Dr. Banner; who had been called away to one of his clinics in Mozambique.

They had decided to wait until tomorrow when the rest of the pack arrived to let the Avengers know what exactly had been going on. As the night gradually wore to a close Skye found herself seated on a couch as Natasha and Clint threw darts at a board halfway across the room while taking shots.

Just as she thinks she is maybe going to fall asleep, she is jarred awake by someone dropping into the seat beside her, looking over she sees Steve sitting there sheepishly as he says "hey, I know this is awkward, but I was wondering if we could talk."

"Ok, sure, what did you want to talk about."

"I wanted to apologise about how I reacted earlier, I was rude, and I had no right to judge what you did. If my mom had still been here, she would have tanned my hide."

"It's ok, Captain, I can't really blame you for feeling the same way I do."

"I'm sorry, but it's not ok. I spoke to Natasha, and she told me a little about what had happened. I just wanted to say, I understand why you did what you did. And I know this probably doesn’t mean much, but I would have done the same thing."

"It means more than you might think Captain" then pausing she continues "I warned Sharon, but I'm going to tell you as well. Be especially careful you don’t hurt Maria, she has a lot of demons in her past, and if you hurt her, you will answer to Tasha and Me. Am I clear Captain?"  
"Yes, Ma'am."  
"Good, then why don’t you go spend some time with your soulmates, I'm sure they would appreciate it."  
"Yes, ma'am."

 

Natasha appears over Skye`s shoulder before placing a kiss on her crown as she says "Hopefully that ends well."

"Maria has had enough pain to last her a lifetime, hopefully, they can help her heal a bit."

"Hopefully, but it won`t be easy. Come on, time for bed we have to be up bright and early tomorrow to see the others in and brief the Avengers on what exactly has been happening."


	24. June 16th

It was the day after their arrival and Skye was laying in bed beside Natasha as she slept silently going over what she had been forced to do on the previous day. Suddenly a voice calls out through the darkness drawing her out of her reverie

"Miss Skye" comes the voice of Jarvis "I have people in the lobby requesting entry they say you and Ms. Romanoff have cleared their entry."

an image is displayed showing pictures side by side of her fellow pack members and Skye says "it's Ok Jarvis, please let them in Natasha, and I will be waiting for them in the common room."

"very good Miss Skye, also Dr. Simmons asked me to tell you she will require some alone time, apparently she has found her soulmate."

"what? Who?"

"it appears her soulmate is Dr. Banner, they ran into each other last night after he returned from Mozambique."

"Ok let Jemma know I got the message and tell her not to worry about it" she pauses and then continues "and Jarvis, tell them congratulations."

 

A groan emerges from Natasha as the redhead says "Skye, Darling, it's too early go back to sleep."

"no can do, Sweetheart. The pack is here, we have to get up before Tony freaks out and finds himself faced with a dozen tired wolves."

"It'd serve him right."

"That might be true, but you know as well as I do they will want to see us before anything else."

"I hate you."

"I know."

"Now who`s quoting Star Wars."

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When they arrive in the common room, they are amazed to find the entire pack passed out on the floor curled around each other. Looking at her mate, Skye can't help but smile at her Family before pulling Natasha down beside the group and going to sleep.

 

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Awakening they find themselves entombed in a pile of bodies as their pack-mates had shifted in recent hours to be closer to them. Breathing out Skye finds a mass of Blonde hair entangled with black hair across her face, her wolf senses immediately identify the scent as coming from Kara, Bobbi and Hunter and to her surprise they detect something else.

It is said that amongst wolves an Alpha can always tell when their pack-mates are bonded and if that bond is complete. It is a sense of the turmoil within the Wolf and for once Skye can't feel that coming off the pair above her. When she had first become an Alpha she could tell Bobbi and Kara were missing soulmates; Bobbi and Hunter were always fighting or fucking, and it was clear their bond was unstable. Whereas Kara had seemed isolated and cold devoid of love almost. So imagine her surprise to find the three of them entangled above her and for once they seemed stable like they all balanced each other out. Leaning over to her mate beside her she taps Natasha's hand before using their neural connection to draw her attention to the triad above them. Aa flare of happiness comes back through the bond, and she is once again reminded that her mate has known these three a lot longer and is clearly happy for them.

Conferring silently with her mate she begins trying to extricate herself from the pile but no matter how she moves she finds the pack moving with them. Deciding enough is enough she reaches up before tickling Bobbi and Kara above her causing them to both waken in spasms of laughter. This quickly causes the entire pack to wake up, and Skye and Natasha manage to extract themselves just before there erupts a massive tickle war, it's actually quite amusing watching some of the deadliest people in the known universe acting like a group of overgrown children.

Eventually, though they all seem to notice Skye and Natasha standing to watch because they are mobbed by the agents from behind them comes a laugh as Phil and Melinda having felt the emotions through the pack bond had come to investigate only to find Natasha and Skye enveloped in a massive group hug

Natasha looks at the mate and can tell this is exactly what she needed to get over the events of the previous day the utterly unquestioning love of the pack has driven all self-doubt from her and wrapped her in a warm blanket of love.

Eventually, though they are forced to break apart as they find themselves the subject of scrutiny from the other tower residents.

 

Looking over Skye can see Stark watching as Pepper Potts stands beside him smiling eventually she manages to make her way over and says "Mr. Stark, Miss Potts I wanted to say thank you for your hospitality, and for letting us bring our family here."

Tony looks squeamish, and you can tell he's not used to this sort of interaction because it's Pepper that answers saying "that’s quite alright, we have more than enough space. Speaking of which as soon as we are done with the briefing we`ll set everyone up in their own Quarters."

"Miss Potts..."

"Please call me Pepper."

I can see Natasha smirking at this as I say "Pepper, I appreciate your offer, but I can't possibly accept, you'll understand why after the briefing but needless to say it wouldn’t be safe for anyone."

"Skye, if I may call you Skye" when I nod my assent she continues "I don’t know if you’ve noticed, but our life isn't the safest at the best of times."  
just as I'm about to interject she holds up her hand "my point is that you being here won't adversely affect our safety, and before you object any further we have plenty of room, and I'm not prepared to take no for an answer."

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They all assemble in the largest lecture theatre Tony has in the tower, because apparently if you can dream it up, he has it. While not particularly big by say University standards, it is large and comfortable with couches and a plush dias for Hulk at the rear. At the moment, the dias is occupied by the pack who lay back and forth in each other's arms, something that appears to be confusing the others greatly, all that is all but for Steve and Sharon.

 

Eventually, when everyone is settled Skye, and Natasha move up to the podium at the front of the room, and Skye says "Jarvis set secure condition 1, and cease all recording."

"Condition 1 set, all accesses secure, all recording ceased."

Looking out Skye says "what I`m about to tell you is highly sensitive, classified level 10 eyes only, or at least it was until 20 hours ago when it was deleted from SHIELD servers."

 

"Project Remus, is a classified SHIELD project attempting to utilise non-invasive genetic engineering to create an enhanced agent. Started by the SSR as an alternative to the Erskine Formula and Project Rebirth in 1938, the project didn't really take off until September 23rd, 1952 when then Agent Peggy Carter was injected with the first prototype of the Remus serum."

As she pauses, Natasha takes over saying "The Remus serum targets a specific strand of DNA only present in about 1% of the population. The serum uses it to enhance their abilities and provides them transmorphological capabilities, namely being able to shift into a second form, that of a wolf."

Tony hearing this laughs saying "you have to be joking, werewolves, not possible" as he turns around he looks toward the Dias where moments earlier sat a group of agents now lay a number of wolves causing Tony to cry out and turn back to Skye and Natasha 

Natasha smirks saying "Told you so, the wolf form is mostly voluntary after the first few changes. So the term werewolf is incorrect, we prefer Homo sapiens-lupus."

As she stops, Skye says "The reason we are telling you this is because every SHIELD agent we have bought here is a member of Project Remus. As of yesterday though we were forced to separate Project Remus from SHIELD." Sighing heavily a moment she continues "There is an infestation problem with SHIELD. We have evidence that HYDRA has infiltrated SHIELD at every level, even up to the World Security Council. It was this that forced our hand."

At this Natasha feeling her mate`s pain over the many deaths says "Project Insight was the name of a secret SHIELD initiative to build a fleet of new and improved helicarriers. The proposed reason being to eliminate terrorist threats before they could be an issue. The real purpose was to kill everyone who would seek to oppose Hydra's policies. It was this Captain, that forced Skye to activate a program to trigger a self-destruct of the Helicarriers while they still remained in their bays."

Suddenly Jarvis says "Incoming priority 1 call from Director Fury."

“put it through Jarvis,” Skye says switching instantly into her Alpha persona "What's going on Director, is everything ok?"

"I found our infiltrators, it was indeed Hydra" pause for effect "As of 0600 hours today I issued SHIELD protocol 117-3 theta. Every SHIELD base in the world was supposed to go into lockdown while its agents were screened for possible links to infiltrator organisations. Instead, there was a breakaway, and approximately 20% of SHIELD personnel abandoned their posts and took arms against their brothers. This breakaway band from all evidence appears to be what is left of Hydra within SHIELD. " he pauses and takes a deep breath letting his anger wash away "According to Intel 2/3 of Hydra's personnel were in the Insight bay when the Helicarriers blew, including Alexander Pierce. They quickly realised they were outnumbered and fled with what resources they could. At present, they have access to only rudimentary SHIELD resources. However, intelligence suggests that Hydra is significantly more diverse than we had first suspected. Stark will enjoy this, but we have evidence that Senator Stern is actually a Hydra agent, as such he has been taken into custody. It is imperative that none of you leave the tower until there is an all-clear message from me, understood."

Tony jumps to his feet "Yes sir, Director Eyepatch sir" he says while jokingly saluting

Skye shoots him a glare, and he instantly falls back into his seat silent as Skye says “understood Director we will wait for your call.”

As soon as the connection is terminated Stark says “what the hell was that Glare for, I have it on good authority you routinely call him Pirate.”

Everyone watches as Skye turns to Tony and says “I call him Pirate because of his tendency to horde powerful items, I do not make fun of him for something that is obviously a reminder of a painful part of his life. How would you feel if we all started calling you Glowstick?”

“I would probably want to throttle you.”

“Then why do you do it to him. You may not like him, but you should at least show common human decency.”

Looking suitably abashed Tony says “Fine, won`t happen again.”

“Good, now back to our briefing. Natasha if you will.”

Smiling at her mate Natasha starts “As we were saying Project insight lead us to the discovery of the infiltration of SHIELD, as of this moment we have removed all Pack members from Shield`s ranks. As of this moment besides this pack there are three others, as of yesterday they each went into hiding. In approximately 9 days they will all converge here to a hidden base formerly from the SSR for a full pack meeting. At this stage, it will be decided what path the pack is to take. Any Questions?”

Steve`s hand is raised as he asks “who`s in-charge of the pack`s at the moment.”

Looking to Melinda Skye says “Mom, do you want to answer that, you know better than I do.”

Melinda stands up before turning to face the others saying “at the moment there are 2 tiers of leaders. The individual pack leaders like Skye and Natasha and the overall pack leaders being Peggy Carter, Angie Martinelli, and Daniel Sousa” at Steve`s stunned look she elaborates “Peggy, Angie, and Daniel are the top tier Alpha`s. As the first awakened they are the oldest and were selected because they had the strongest incidence of the Remus Gene. Next, after them are the secondary Alphas like Skye and Natasha, they oversee the day to day operations of the pack and are only answerable to Peggy, Angie, and Daniel. Back when Phil and I were Alphas we only ever met them once, it is extremely rare for them to take an active hand in the subdivisions of the packs.”

Tony, this time, calls out “wait, what do you mean when you and Agent were alphas, I thought there were only 2 alphas to a pack.”

Glaring lightly at Stark for interrupting Melinda says “when a wolf is mortally injured their wolf can give itself to save them. During New York Phil`s wolf did just that. While it is possible to resurrect the wolf, by our laws it can never be an Alpha ever again and as Phil`s Bond mate I stepped down as well.”

“Yeah, ok, but how come Little Red and Mini-me are the Alphas now, wouldn’t it have gone to say Hill,” Stark asks looking at Skye and Natasha

“You're correct, normally it would have gone to Maria. However, Natasha and I are Bonded, and for some reason only a few weeks after I was awoken I was already as strong as an Alpha; therefore, we became the pack Alphas”

“So what does this all actually mean,” asks Darcy  
“in simplest terms, we are stronger faster and overall more resilient than the normal human. The reason we are here is that we can`t allow Hydra to find out about this, it would mean the utter destabilisation of the world.”  
Pepper rises from her seat, and Natasha can feel Skye’s worry that she is going to send them packing but instead she says “in that case lets go see about those quarters.”


	25. discontinuance note

**Summary for the Chapter:**

> i am sorry to say i am placing this story on indefinate hiatus, if you want to have a go at it please send me a message. i will likely continue it at some stage but for the moment there will not be a regular update schedule

i am sorry to say i am placing this story on indefinate hiatus, if you want to have a go at it please send me a message. i will likely continue it at some stage but for the moment there will not be a regular update schedule


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